Supplement 1. R code for fitting the N-mixture model.

<h2>File List</h2><div> <a href="BetaBnCountsTruncPoissonAbund.R">BetaBnCountsTruncPoissonAbund.R</a> (MD5: 8dbe29e76e78687fcb479dce7b3e2424)</div><h2>Description</h2><div> <p>BetaBnCountsTruncPoissonAbund.R contains R code for simulating point counts under the assumptions of the <i>N</i>-mixture model and for computing maximum-likelihood estimates of the model's parameters.</p> </div

Appendix C. Pearson residuals of models used in cross-validation.

Pearson residuals of models used in cross-validation

Appendix D. Plot of Pearson residuals for models used in cross-validation.

Plot of Pearson residuals for models used in cross-validation

Appendix B. Parametric bootstrapping to estimate uncertainty of plot-level abundance.

Parametric bootstrapping to estimate uncertainty of plot-level abundance

Results of generalized linear mixed models (GLMMs) showing the probability (<i>P</i>_<i>t</i>) of a manatee being above a 1.25-m threshold for striking depth by watercraft and effect size (ES) with standard deviations (SD) and 95% credible intervals (CI) in relation to habitat features, time of day, and travel speed category.

<p>Results of generalized linear mixed models (GLMMs) showing the probability (<i>P</i>_<i>t</i>) of a manatee being above a 1.25-m threshold for striking depth by watercraft and effect size (ES) with standard deviations (SD) and 95% credible intervals (CI) in relation to habitat features, time of day, and travel speed category.</p

Map of Tampa Bay, FL, U.S.A. with bathymetry, known waterways, seagrass and GPS locations (by color) for nine manatees.

<p>Map of Tampa Bay, FL, U.S.A. with bathymetry, known waterways, seagrass and GPS locations (by color) for nine manatees.</p

Summary of manatee age–sex class, TDR deployment duration, and movement and diving behavior.

<p>The number, duration and distance of sorties, maximum time between sorties, mean and maximum velocities outside of the discharge canal and standard deviations are given for the entire GPS tag deployment duration. Time spent outside of the power plant’s no-boat-entry canal, mean and maximum dive depths, and proportion of depth records ≤1.25 m, are given for the period of TDR data collection.</p

Proportion of depth records (vertical bars), with standard deviations, in relation to substrate, movement category, time of day, depth categories, and proximity to a waterway.

<p>GLMM probabilities (<i>P</i>_<i>t</i>) of being within striking depth (≤1.25m) are shown for each with 95% credible intervals (circles).</p

Influence of Manatees' Diving on Their Risk of Collision with Watercraft - Fig 4

<p>A.) Mean depth (m) for all dive records recorded by time-depth recorders (n = 9) by hour with standard deviations; horizontal line is striking depth. B.) Proportion of fast travel movement records by hour with standard deviations. C.) Mean depth (m) during fast and slow travel movements with standard deviations.</p

Dive profile of manatee TTB108 crossing Tampa Bay (west shoreline to Tampa Electric Company’s Big Bend Power Station) from 04:47:55 to 16:47:15 EST, January 31, 2004.

<p>Dashed line depicts water temperature recorded by time-depth recorder.</p